How do you remove these nuts? special tool?

 

is this a manual transmission ?

 

No, It's an automatic.

 

Pulling the engine. This is looking thru the starter hole.

 

You remove the nut, not the stud. The stud is installed onto the torque convertor.

I imagine the studs were put in place so that assembly on the line is easier. Much simpler to turn the convertor a little bit to align the 4 studs vs trying to blindly find them

There should be four studs you'll need to remove the nuts from. After that, the convertor should come off with the transmission

 

The picture looks like the nut is gone already, look at another stud